I believe that Sam's aura waves thingys are connected with Billy Jeans in an unusual way so that he can feel the pregnacy. The third thing you pointed out however contradicts itself because if its a soul exhange than how does she have a womb from the baby to disappear from since she would be in a man's body?

*blinks* Good point. We were all so focused on Sam, no one really thought about things from Billie Jean's side. And I agree with the 'connection' with Billie Jean - after all, it's something Sam has done in later seasons, and it is kinda necessary, otherwise there's no way that Sam could convincingly pull off being a pregnant girl!

But, anyway, in answer to the main question posed, I prefer the body leaping theory. It's what I always assumed anyway, from the handful of episodes I initially saw, and it just appeals to me.

And, on a side note, thanks HologramIAm for sharing the comic pages. I have the whole set, but mine are in storage, and I really miss them. *sigh* If only I could draw; I'd do fan-produced comics myself.